Variant report

Variant	rs12902947
Chromosome Location	chr15:33303758-33303759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:33297830..33309224-chr15:33355310..33362883,25	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248905	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10519771	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630735	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11631942	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11637416	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637853	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12899665	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16962859	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16962944	1.00[CEU][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17229048	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs28373061	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28404179	0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28436666	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28548712	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34331348	0.88[ASN][1000 genomes]
rs35978285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494831	0.92[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6494832	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv456785	chr15:32926076-33352989	Genic enhancers Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv568913	chr15:32926076-33352989	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv903978	chr15:33144202-33308641	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv903979	chr15:33144202-33550256	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv1041609	chr15:33148035-33355999	Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv542339	chr15:33148035-33355999	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv1052966	chr15:33149753-33541951	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv542340	chr15:33149753-33541951	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
9	nsv568917	chr15:33167171-33304172	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
10	nsv903981	chr15:33207082-33550256	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv568918	chr15:33244672-33446971	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1047542	chr15:33282673-33307206	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
14	nsv1036917	chr15:33284701-33312362	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	esv2761862	chr15:33284713-33312374	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33288800-33309200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr15:33299800-33305200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:33300400-33314200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:33300600-33314400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr15:33301200-33305800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr15:33301200-33306400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:33301200-33308800	Weak transcription	Aorta	Aorta
8	chr15:33301600-33304400	Weak transcription	HSMMtube	muscle
9	chr15:33301600-33305400	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr15:33301600-33305600	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr15:33301600-33305800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr15:33301600-33305800	Weak transcription	NH-A	brain
13	chr15:33301600-33305800	Weak transcription	Osteobl	bone
14	chr15:33301600-33306000	Weak transcription	NHDF-Ad	bronchial
15	chr15:33301600-33306200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr15:33301600-33306200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:33301600-33306400	Weak transcription	Stomach Mucosa	stomach
18	chr15:33301600-33308800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr15:33301600-33314400	Weak transcription	Gastric	stomach
20	chr15:33301800-33304000	Weak transcription	Thymus	Thymus
21	chr15:33301800-33304200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:33301800-33306000	Weak transcription	NHLF	lung
23	chr15:33302000-33304200	Weak transcription	HSMM	muscle
24	chr15:33302200-33314400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:33302400-33304200	Weak transcription	Fetal Thymus	thymus
26	chr15:33303400-33304200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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